Merge pull request #5 from EBISPOT/develop

EBISPOT · May 14, 2020 · 78dd0dc · 78dd0dc
2 parents 116aa44 + cf41ff7
commit 78dd0dc
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Showing 92 changed files with 2,379 additions and 552 deletions.
diff --git a/build.sh b/build.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+docker build --force-rm=true -t gwas-deposition-backend:latest .
+docker tag gwas-deposition-backend:latest ebispot/gwas-deposition-backend:latest-sandbox
+docker push ebispot/gwas-deposition-backend:latest-sandbox
diff --git a/deploy.sh b/deploy.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+kubectl delete deploy gwas-deposition-backend -n gwas
+kubectl apply -f /home/tudor/Desktop/_deployment_plans_/gwas-deposition-backend-deployment.yaml
diff --git a/pom.xml b/pom.xml
@@ -14,7 +14,7 @@
     <parent>
         <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
         <artifactId>gwasdepo-master</artifactId>
-        <version>1.0.0</version>
+        <version>1.0.1-SNAPSHOT</version>
     </parent>
 
     <properties>
@@ -66,7 +66,7 @@
         <dependency>
             <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
             <artifactId>gwasdepo-commons</artifactId>
-            <version>1.0.0</version>
+            <version>1.0.4-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
@@ -136,6 +136,10 @@
             <groupId>commons-fileupload</groupId>
             <artifactId>commons-fileupload</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.modelmapper</groupId>
+            <artifactId>modelmapper</artifactId>
+        </dependency>
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/Application.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/Application.java
@@ -6,12 +6,11 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 import uk.ac.ebi.spot.gwas.deposition.config.SystemConfigProperties;
-import uk.ac.ebi.spot.gwas.deposition.constants.GWASDepositionBackendConstants;
+import uk.ac.ebi.spot.gwas.deposition.constants.GeneralCommon;
 
 import javax.annotation.PostConstruct;
 import javax.annotation.PreDestroy;
@@ -40,7 +39,7 @@ public void destroy() {
 
     public static void main(String[] args) throws UnknownHostException {
         String hostAddress = InetAddress.getLocalHost().getHostAddress();
-        String logFileName = System.getenv(GWASDepositionBackendConstants.LOG_FILE_NAME);
+        String logFileName = System.getenv(GeneralCommon.LOG_FILE_NAME);
         System.setProperty("log.file.name", logFileName + "-" + hostAddress);
         SpringApplication.run(Application.class, args);
     }

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/components/BodyOfWorkListener.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/components/BodyOfWorkListener.java
@@ -0,0 +1,37 @@
+package uk.ac.ebi.spot.gwas.deposition.components;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.annotation.Async;
+import org.springframework.stereotype.Component;
+import uk.ac.ebi.spot.gwas.deposition.domain.BodyOfWork;
+import uk.ac.ebi.spot.gwas.deposition.domain.BodyOfWorkWatch;
+import uk.ac.ebi.spot.gwas.deposition.domain.Submission;
+import uk.ac.ebi.spot.gwas.deposition.repository.BodyOfWorkWatchRepository;
+
+import java.util.Optional;
+
+@Component
+public class BodyOfWorkListener {
+
+    @Autowired
+    private BodyOfWorkWatchRepository bodyOfWorkWatchRepository;
+
+    @Async
+    public void update(BodyOfWork bodyOfWork) {
+        Optional<BodyOfWorkWatch> bodyOfWorkWatchOptional = bodyOfWorkWatchRepository.findByBowId(bodyOfWork.getBowId());
+        if (bodyOfWorkWatchOptional.isPresent()) {
+            BodyOfWorkWatch bodyOfWorkWatch = bodyOfWorkWatchOptional.get();
+            bodyOfWorkWatch.setVisited(false);
+            bodyOfWorkWatchRepository.save(bodyOfWorkWatch);
+        }
+    }
+
+    public void update(Submission submission) {
+        if (submission.getBodyOfWorks() != null) {
+            if (!submission.getBodyOfWorks().isEmpty()) {
+                String bowId = submission.getBodyOfWorks().get(0);
+                bodyOfWorkWatchRepository.insert(new BodyOfWorkWatch(bowId));
+            }
+        }
+    }
+}
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/BackendMailConfig.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/BackendMailConfig.java
@@ -0,0 +1,36 @@
+package uk.ac.ebi.spot.gwas.deposition.config;
+
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+@Component
+public class BackendMailConfig {
+
+    @Value("${gwas-deposition.email-config.subject}")
+    private String subject;
+
+    @Value("${gwas-deposition.email-config.emails.success}")
+    private String successEmail;
+
+    @Value("${gwas-deposition.email-config.emails.fail}")
+    private String failEmail;
+
+    @Value("${gwas-deposition.email-config.base-url}")
+    private String submissionsBaseURL;
+
+    public String getSubmissionsBaseURL() {
+        return submissionsBaseURL;
+    }
+
+    public String getSubject() {
+        return subject;
+    }
+
+    public String getSuccessEmail() {
+        return successEmail;
+    }
+
+    public String getFailEmail() {
+        return failEmail;
+    }
+}
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/BackendQuartzConfig.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/BackendQuartzConfig.java
@@ -31,6 +31,9 @@ public class BackendQuartzConfig {
     @Autowired(required = false)
     private SOLRDocumentStatusCheckConfigSandbox solrDocumentStatusCheckConfigSandbox;
 
+    @Autowired(required = false)
+    private CompleteSubmissionsConfig completeSubmissionsConfig;
+
     @PostConstruct
     private void initialize() throws SchedulerException {
         if (statsConfig != null) {
@@ -51,6 +54,9 @@ private void initialize() throws SchedulerException {
         if (solrDocumentStatusCheckConfigSandbox != null) {
             quartzSchedulerJobConfig.addJob(solrDocumentStatusCheckConfigSandbox);
         }
+        if (completeSubmissionsConfig != null) {
+            quartzSchedulerJobConfig.addJob(completeSubmissionsConfig);
+        }
         quartzSchedulerJobConfig.initializeJobs();
     }
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/ExceptionHandlerAdvice.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/ExceptionHandlerAdvice.java
@@ -34,6 +34,13 @@ public ResponseEntity<String> handleSubmissionOnUnacceptedPublicationTypeExcepti
         return new ResponseEntity<>(e.getMessage(), headers, HttpStatus.BAD_REQUEST);
     }
 
+    @ExceptionHandler(InvalidSubmissionTypeException.class)
+    public ResponseEntity<String> handleInvalidSubmissionTypeExceptionException(InvalidSubmissionTypeException e) {
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.TEXT_PLAIN);
+        return new ResponseEntity<>(e.getMessage(), headers, HttpStatus.BAD_REQUEST);
+    }
+
     @ExceptionHandler(SSGlobusFolderCreatioException.class)
     public ResponseEntity<String> handleSSGlobusFolderCreatioException(SSGlobusFolderCreatioException e) {
         HttpHeaders headers = new HttpHeaders();
@@ -55,6 +62,20 @@ public ResponseEntity<String> handleCannotDeleteSSTemplateFileException(CannotDe
         return new ResponseEntity<>(e.getMessage(), headers, HttpStatus.BAD_REQUEST);
     }
 
+    @ExceptionHandler(CannotDeleteBodyOfWorkException.class)
+    public ResponseEntity<String> handleCannotDeleteBodyOfWorkException(CannotDeleteBodyOfWorkException e) {
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.TEXT_PLAIN);
+        return new ResponseEntity<>(e.getMessage(), headers, HttpStatus.BAD_REQUEST);
+    }
+
+    @ExceptionHandler(CannotCreateSubmissionOnExistingBodyOfWork.class)
+    public ResponseEntity<String> handleCannotCreateSubmissionOnExistingBodyOfWork(CannotCreateSubmissionOnExistingBodyOfWork e) {
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.TEXT_PLAIN);
+        return new ResponseEntity<>(e.getMessage(), headers, HttpStatus.BAD_REQUEST);
+    }
+
     @ExceptionHandler(DeleteOnSubmittedSubmissionNotAllowedException.class)
     public ResponseEntity<String> handleDeleteOnSubmittedSubmissionNotAllowedException(DeleteOnSubmittedSubmissionNotAllowedException e) {
         HttpHeaders headers = new HttpHeaders();

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/GWASDepositionBackendConfig.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/GWASDepositionBackendConfig.java
@@ -30,11 +30,11 @@ public class GWASDepositionBackendConfig {
     @Value("${gwas-deposition.proxy-prefix:#{NULL}}")
     private String proxyPrefix;
 
-    @Value("${gwas-deposition.email-config.base-url}")
-    private String submissionsBaseURL;
+    @Value("${gwas-deposition.db:#{NULL}}")
+    private String dbName;
 
-    public String getSubmissionsBaseURL() {
-        return submissionsBaseURL;
+    public String getDbName() {
+        return dbName;
     }
 
     public boolean isAuthEnabled() {

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/MailConfig.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/MailConfig.java
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/MongoConfig.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/config/MongoConfig.java
@@ -4,7 +4,6 @@
 import com.mongodb.MongoClientURI;
 import com.mongodb.ServerAddress;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Profile;
@@ -61,9 +60,12 @@ public static class MongoConfigSandbox extends AbstractMongoConfiguration {
         @Autowired
         private SystemConfigProperties systemConfigProperties;
 
+        @Autowired
+        private GWASDepositionBackendConfig gwasDepositionBackendConfig;
+
         @Override
         protected String getDatabaseName() {
-            return systemConfigProperties.getDbName();
+            return gwasDepositionBackendConfig.getDbName();
         }
 
         @Bean
@@ -87,9 +89,12 @@ public static class MongoConfigProd extends AbstractMongoConfiguration {
         @Autowired
         private SystemConfigProperties systemConfigProperties;
 
+        @Autowired
+        private GWASDepositionBackendConfig gwasDepositionBackendConfig;
+
         @Override
         protected String getDatabaseName() {
-            return systemConfigProperties.getDbName();
+            return gwasDepositionBackendConfig.getDbName();
         }
 
         @Bean
@@ -115,4 +120,45 @@ public MongoClient mongoClient() {
             return new MongoClient(new MongoClientURI("mongodb://" + credentials + mongoUri));
         }
     }
+
+    @Configuration
+    @EnableMongoRepositories(basePackages = {"uk.ac.ebi.spot.gwas.deposition.repository"})
+    @EnableTransactionManagement
+    @Profile({"gcp-sandbox"})
+    public static class MongoConfiGCPSandbox extends AbstractMongoConfiguration {
+
+        @Autowired
+        private SystemConfigProperties systemConfigProperties;
+
+        @Autowired
+        private GWASDepositionBackendConfig gwasDepositionBackendConfig;
+
+        @Override
+        protected String getDatabaseName() {
+            return gwasDepositionBackendConfig.getDbName();
+        }
+
+        @Bean
+        public GridFsTemplate gridFsTemplate() throws Exception {
+            return new GridFsTemplate(mongoDbFactory(), mappingMongoConverter());
+        }
+
+        @Override
+        public MongoClient mongoClient() {
+            String mongoUri = systemConfigProperties.getMongoUri();
+            String dbUser = systemConfigProperties.getDbUser();
+            String dbPassword = systemConfigProperties.getDbPassword();
+            String credentials = "";
+            if (dbUser != null && dbPassword != null) {
+                dbUser = dbUser.trim();
+                dbPassword = dbPassword.trim();
+                if (!dbUser.equalsIgnoreCase("") &&
+                        !dbPassword.equalsIgnoreCase("")) {
+                    credentials = dbUser + ":" + dbPassword + "@";
+                }
+            }
+
+            return new MongoClient(new MongoClientURI("mongodb+srv://" + credentials + mongoUri));
+        }
+    }
 }